Collagen Structure

ANRV378-BI78-32 ARI 5 May 2009 15:11

Collagen Structureand StabilityMatthew D. Shoulders1 and Ronald T. Raines1,2

1Department of Chemistry and 2Department of Biochemistry, University of Wisconsin,Madison, Wisconsin 53706; email: [email protected]

Annu. Rev. Biochem. 2009. 78:929–58

First published online as a Review in Advance onApril 3, 2009

The Annual Review of Biochemistry is online atbiochem.annualreviews.org

This article’s doi:10.1146/annurev.biochem.77.032207.120833

Copyright c© 2009 by Annual Reviews.All rights reserved

0066-4154/09/0707-0929$20.00

Key Words

biomaterials, extracellullar matrix, fibrillogenesis, proline,stereoelectronic effects, triple helix

AbstractCollagen is the most abundant protein in animals. This fibrous, struc-tural protein comprises a right-handed bundle of three parallel, left-handed polyproline II-type helices. Much progress has been made inelucidating the structure of collagen triple helices and the physicochem-ical basis for their stability. New evidence demonstrates that stereoelec-tronic effects and preorganization play a key role in that stability. Thefibrillar structure of type I collagen—the prototypical collagen fibril—has been revealed in detail. Artificial collagen fibrils that display someproperties of natural collagen fibrils are now accessible using chemicalsynthesis and self-assembly. A rapidly emerging understanding of themechanical and structural properties of native collagen fibrils will guidefurther development of artificial collagenous materials for biomedicineand nanotechnology.

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ECM: extracellularmatrix

PPII: polyproline IItype

Hyp: (2S,4R)-4-hydroxyproline

Tropocollagen (TC):the monomericcollagen triple helixafter proteolysis ofcollagen propeptides

Contents

INTRODUCTION . . . . . . . . . . . . . . . . . . 930STRUCTURE OF THE

COLLAGEN TRIPLE HELIX . . . . 930UNDERSTANDING

TRIPLE-HELIX STRUCTUREAND STABILITY . . . . . . . . . . . . . . . . . 934Interstrand Hydrogen Bonds . . . . . . . 935Glycine Substitutions . . . . . . . . . . . . . . 935Prolines in the Xaa

and Yaa Positions . . . . . . . . . . . . . . . 936Role of Hyp . . . . . . . . . . . . . . . . . . . . . . . 937Proline Derivatives in the Xaa

Position . . . . . . . . . . . . . . . . . . . . . . . . 940An n→π∗ Interaction . . . . . . . . . . . . . . 941Hyp in the Xaa Position . . . . . . . . . . . . 942Heterotrimeric Synthetic

Triple Helices . . . . . . . . . . . . . . . . . . 942Nonproline Substitutions

in the Xaa and Yaa Positions . . . . . 944HIGHER-ORDER COLLAGEN

STRUCTURE . . . . . . . . . . . . . . . . . . . . 944Fibril Structure . . . . . . . . . . . . . . . . . . . . 944Nucleation and Modulation

of Collagen Fibrillogenesis . . . . . . 946MECHANICAL PROPERTIES

OF COLLAGEN FIBRILS . . . . . . . . 946COLLAGENOUS

BIOMATERIALS . . . . . . . . . . . . . . . . . 947Collagen via Chemical Synthesis . . . . 947Biological and Biomedical

Applications of SyntheticCollagen . . . . . . . . . . . . . . . . . . . . . . . 948

INTRODUCTION

Collagen is an abundant structural protein in allanimals. In humans, collagen comprises one-third of the total protein, accounts for three-quarters of the dry weight of skin, and is themost prevalent component of the extracellu-lar matrix (ECM). Twenty-eight different typesof collagen composed of at least 46 distinctpolypeptide chains have been identified in ver-tebrates, and many other proteins contain col-lagenous domains (1, 2). Remarkably, intact

collagen has been discovered in soft tissue of thefossilized bones of a 68 million-year-old Tyran-nosaurus rex fossil (3, 4), by far the oldest proteindetected to date. That discovery is, however,under challenge (5, 6).

The defining feature of collagen is an el-egant structural motif in which three parallelpolypeptide strands in a left-handed, polypro-line II-type (PPII) helical conformation coilabout each other with a one-residue staggerto form a right-handed triple helix (Figure 1).The tight packing of PPII helices within thetriple helix mandates that every third residuebe Gly, resulting in a repeating XaaYaaGlysequence, where Xaa and Yaa can be anyamino acid. This repeat occurs in all typesof collagen, although it is disrupted at cer-tain locations within the triple-helical domainof nonfibrillar collagens (8). The amino acidsin the Xaa and Yaa positions of collagen areoften (2S )-proline (Pro, 28%) and (2S,4R)-4-hydroxyproline (Hyp, 38%), respectively.ProHypGly is the most common triplet(10.5%) in collagen (9). In animals, individualcollagen triple helices, known as tropocollagen(TC), assemble in a complex, hierarchical man-ner that ultimately leads to the macroscopicfibers and networks observed in tissue, bone,and basement membranes (Figure 2).

The categories of collagen include the clas-sical fibrillar and network-forming collagens,the FACITs (fibril-associated collagens with in-terrupted triple helices), MACITs (membrane-associated collagens with interrupted triplehelices), and MULTIPLEXINs (multipletriple-helix domains and interruptions). Colla-gen types, their distribution, composition, andpathology are listed in Table 1. It is notewor-thy that, although the three polypeptide chainsin the triple helix of each collagen type can beidentical, heterotrimeric triple helices are moreprevalent than are homotrimeric triple helices.

STRUCTURE OF THECOLLAGEN TRIPLE HELIX

In 1940, Astbury & Bell (11) proposed thatthe collagen molecule consists of a single

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extended polypeptide chain with all amidebonds in the cis conformation. A significant ad-vance was achieved when, in the same 1951 is-sue of the Proceedings of the National Academy ofSciences in which they put forth the correctstructures for the α-helix and β-sheet, Pauling& Corey (12) proposed a structure for colla-gen. In that structure, three polypeptide strandswere held together in a helical conformationby hydrogen bonds. Within each amino acidtriplet, those hydrogen bonds engaged fourof the six main chain heteroatoms, and theirformation required two of the three peptidebonds to be in the cis conformation. In 1954,Ramachandran & Kartha (13, 14) advanced astructure for the collagen triple helix on thebasis of fiber diffraction data. Their structurewas a right-handed triple helix of three stag-gered, left-handed PPII helices with all peptidebonds in the trans conformation and two hy-drogen bonds within each triplet. In 1955, thisstructure was refined by Rich & Crick (15–16)and by North and coworkers (17) to the triple-helical structure accepted today, which has asingle interstrand N–H(Gly)· · ·O==C(Xaa) hydro-gen bond per triplet and a tenfold helical sym-metry with a 28.6-A axial repeat (10/3 helicalpitch) (Figure 1).

Fiber diffraction studies cannot reveal thestructure of collagen at atomic resolution.Exacerbating this difficulty, the large size, in-solubility, repetitive sequence, and complex hi-erarchical structure of native collagen thwartmost biochemical and biophysical analyses.Hence, a reductionist approach using triple-helical, collagen-related peptides (CRPs) hasbeen employed extensively since the late 1960s(18).

In 1994, Berman and coworkers (19) re-ported the first high-resolution crystal struc-ture of a triple-helical CRP (Figure 1a). Thisstructure confirmed the existence of inter-strand N–H(Gly)· · ·O==C(Xaa) hydrogen bonds(Figure 1c,d ) and provided additional insights,including that Cα–H(Gly/Yaa)· · ·O==C(Xaa/Gly) hy-drogen bonds could likewise stabilize the triplehelix (20). Using CRPs and X-ray crystal-lography, the structural impact of a single

N1

a b

N1c

N2

N3

Hyp

Gly

Pro

HypC2C1

C3

dN1 N2 N3

HypHyp

Hyp

ProC=O ProC=O

Pro

Gly

GlyN–H

H–NGly

C1 C2 C3

H–NGly

O=CPro

Hyp

Figure 1Overview of the collagen triple helix. (a) First high-resolution crystal structureof a collagen triple helix, formed from (ProHypGly)4–(ProHypAla)–(ProHypGly)5 [Protein Data Bank (PDB) entry 1cag] (19). (b) View down theaxis of a (ProProGly)10 triple helix [PDB entry 1k6f (7)] with the three strandsdepicted in space-filling, ball-and-stick, and ribbon representation. (c) Ball-and-stick image of a segment of collagen triple helix [PDB entry 1cag (19)],highlighting the ladder of interstrand hydrogen bonds. (d ) Stagger of the threestrands in the segment in panel c.

CRP: collagen-relatedpeptide

Gly → Ala substitution was observed (19), theeffects of neighboring charged residues in atriple helix were analyzed (21), and a snapshotof the interaction of a triple-helical CRP withthe I domain of integrin α2β1 was obtained(Figure 3) (22).

Most X-ray crystallographic studies onCRPs have been performed on proline-richcollagenous sequences. All of the resultingstructures have a 7/2 helical pitch (20.0-A axialrepeat), in contrast to the 10/3 helical pitch(28.6-A axial repeat) predicted for naturalcollagen by fiber diffraction (17). On thebasis of X-ray crystal structures of proline-rich

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≤0.8 nm

∼300 nmProtocollagen strand

N- and C-terminalpropeptides

P4H, P3HLysyl hydroxylase

Protein disulfide isomerase

1–2 nm

∼300 nmProcollagen triple helix

≤300 nmTropocollagen triple helix

ProcollagenN- and C-proteinases

<5 nm

Overlap: 0.46DGap: 0.54D

D = 67 nm

Collagen microfibril≤1 cm

Collagen fiber

≤500 nmLysyl oxidase

SSSS

5 µm

Skin

Collagen genes

Self-assembly

Desmosine Isodesmosine

N+

HN

HN

HN NH

O

O

O

O

N+

HN

HN

NH

NH

O

O

OO

N- and C-terminaltelopeptides

Cross-linking

Figure 2Biosynthetic route to collagen fibers (110), which are the major component of skin. Size and complexity areincreased by posttranslational modifications and self-assembly. Oxidation of lysine side chains leads to thespontaneous formation of desmosine and isodesmosine cross-links.

CRPs, and in accordance with an early proposalregarding the helical pitch of natural triplehelices (23), Okuyama and coworkers (24)postulated that the correct average helicalpitch for natural collagen is 7/2. The generality

of this hypothesis is unclear, as few regions ofnatural collagen are as proline rich as the CRPsanalyzed by X-ray crystallography. The actualhelical pitch of collagen likely varies acrossthe domains and types of natural collagen.


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Table 1 Vertebrate collagensa

Type Class Composition Distributionb Pathologyc

I Fibrillar α1[I]2α2[I] Abundant and widespread: dermis,bone, tendon, ligament

OI, Ehlers–Danlos syndrome,osteoporosis

II Fibrillar α1[II]3 Cartilage, vitreous Osteoarthrosis, chondrodysplasiasIII Fibrillar α1[III]3 Skin, blood vessels, intestine Ehlers-Danlos syndrome, arterial

aneurysmsIV Network α1[IV]2α2[IV] Basement membranes Alport syndrome

α3[IV]α4[IV]α5[IV]α5[IV]2α6[IV]

V Fibrillar α1[V]3 Widespread: bone, dermis, cornea,placenta

Ehlers-Danlos syndromeα1[V]2α2[V]

α1[V]α2[V]α3[V]VI Network α1[VI]α2[VI] α3[VI]d Widespread: bone, cartilage, cornea,

dermisBethlem myopathy

α1[VI]α2[VI] α4[VI]VII Anchoring fibrils α1[VII]2α2[VII] Dermis, bladder Epidermolysis bullosa acquisitaVIII Network α1[VIII]3 Widespread: dermis, brain, heart,

kidneyFuchs endothelia corneal dystrophy

α2[VIII]3

α1[VIII]2α2[VIII]IX FACITe α1[IX]α2[IX]α3[IX] Cartilage, cornea, vitreous Osteoarthrosis, multiple epiphyseal

dysplasiaX Network α1[X]3 Cartilage ChondrodysplasiaXI Fibrillar α1[XI]α2[XI]α3[XI] Cartilage, intervertebral disc Chondrodysplasia, osteoarthrosisXII FACIT α1[XII]3 Dermis, tendon —XIII MACIT — Endothelial cells, dermis, eye, heart —XIV FACIT α1[XIV]3 Widespread: bone, dermis, cartilage —XV MULTIPLEXIN — Capillaries, testis, kidney, heart —XVI FACIT — Dermis, kidney —XVII MACIT α1[XVII]3 Hemidesmosomes in epithelia Generalized atrophic epidermolysis

bullosaXVIII MULTIPLEXIN — Basement membrane, liver Knobloch syndromeXIX FACIT — Basement membrane —XX FACIT — Cornea (chick) —XXI FACIT — Stomach, kidney —XXII FACIT — Tissue junctions —XXIII MACIT — Heart, retina —XXIV Fibrillar — Bone, cornea —XXV MACIT — Brain, heart, testis Amyloid formation?XXVI FACIT — Testis, ovary —XXVII Fibrillar — Cartilage —XXVIIIf — — Dermis, sciatic nerve Neurodegenerative disease?

aInformation is updated from References 1 and 32.bPartial listing of tissues in which the relevant collagen type occurs.cFor a discussion of the role of specific collagen types in human disease, see Reference 32.dα4[VI], α5[VI], and α6[VI] chains were reported in 2008 (10), but the composition of triple helices containing α5[VI] and α6[VI] is unknown.eAbbreviations: FACIT, fibril-associated collagen with interrupted triple helices; MACIT, membrane-associated collagen with interrupted triple helices;MULTIPLEXIN, multiple triple-helix domains and interruptions.fCollagen XXVIII was reported in 2006 (2).


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a

b

c

}

Region where Ala residues replaceGly residues in the (XaaYaaGly) repeat

GluCo2+

Figure 3Snapshots of interesting crystal structures of collagen triple helices. (a) Impact of a Gly→Ala substitution onthe structure of a collagen triple helix formed from the collagen-related peptide (CRP) (ProHypGly)4–(ProHypAla)–(ProHypGly)5 [Protein Data Bank (PDB) entry 1cag (19)]. The Ala residues (red ) disturb thestructure. Mutations leading to such structural irregularities are common in osteogenesis imperfecta and canbe lethal. (b) Depiction of the effect of a single GluLysGly triplet on the packing of neighboringtriple-helical CRPs in crystalline (ProHypGly)4–(GluLysGly)–(ProHypGly)5 [PDB entry 1qsu (21)]. Theaxial stagger of the individual triple helices, which is presumably compelled by deleterious Coulombicinteractions between charged residues, is reminiscent of the D-periodic structure in collagen fibrils. Similarinteractions could contribute to the morphology of collagen fibrils. (c) Triple-helical CRP containing theintegrin-binding domain GFOGER in complex with the I domain of integrin α2β1 [PDB entry 1dzi (22)].The bend in the triple helix is thought to arise from the protein-protein interaction. A Glu residue in themiddle strand of the triple helix coordinates to cobalt(II) bound in the I domain of integrin α2β1.

Specifically, the helical pitch could be 10/3 inproline-poor regions and 7/2 in proline-rich re-gions. This proposal is supported by the obser-vation that proline-poor regions within crys-talline CRPs occasionally display a 10/3 helicalpitch (25, 26). Variability in the triple-helicalpitch of native collagen could play a role in theinteraction of collagenous domains with otherbiomolecules (22, 27–29).

UNDERSTANDINGTRIPLE-HELIX STRUCTUREAND STABILITY

The vital importance of collagen as a scaffoldfor animals demands a manifold of essentialcharacteristics. These characteristics includethermal stability, mechanical strength, and theability to engage in specific interactions with


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other biomolecules. Understanding how suchproperties are derived from the fundamentalstructural unit of collagen—the triple helix—necessitates a comprehensive knowledge of themechanisms underlying triple-helix structureand stability.

Interstrand Hydrogen Bonds

The ubiquity of collagen makes the ladderof recurrent N–H(Gly)· · ·O==C(Xaa) hydro-gen bonds that form within the triple helix(Figure 1c,d ) the most abundant amide–amidehydrogen bond in kingdom Animalia. Replac-ing the Yaa–Gly amide bond with an esterin a host-guest CRP (Figure 4a,b) enabledestimation of the strength of each amide–amidehydrogen bond as �G◦ = −2.0 kcal/mol (30).Boryskina and coworkers (31) used a varietyof other experimental techniques to assess thissame parameter, estimating the strength ofeach amide–amide hydrogen bond within apoly(GlyProPro) CRP as �G◦ = −1.8 kcal/moland within native collagen as �G◦ =−1.4 kcal/mol.

Glycine Substitutions

Numerous collagen-related diseases are associ-ated with mutations in both triple-helical andnontriple-helical domains of various collagens(Table 1). These diseases have been reviewedin detail elsewhere (32) and are not discussedextensively herein.

The Gly residue in the XaaYaaGly repeat isinvariant in natural collagen, and favorable sub-stitutions are unknown in CRPs (33). A compu-tational study suggested that replacing the obli-gate Gly residues of collagen with d-alanine ord-serine would stabilize the triple helix (34) andthus that the Gly residues in collagen are surro-gates for nonnatural d-amino acids. Subsequentexperimental data demonstrated, however, thatthis notion was erroneous (35).

Many of the most damaging mutationsto collagen genes result in the replacementof a Gly residue within the triple helix(Figure 1c,d ). Both the identity of the amino

c

3S-Hyp

Amide bond

d

a b

Ester isostere

CH2

N

N

O

NH

O

F

N

NCH2

ON

O

FN

N

NCH2

O

O

F

O

O F

FO F

H

H

δ –

δ –δ –

N

NO

H

O

NO

NH

O

N

NO

O

Xaa

XaaYaa

Yaa

N

OO

O

NO

NH

O

N

NO

O

Xaa

XaaYaa

Yaa

Figure 4Importance of interstrand hydrogen bonds for collagen triple-helix stability.(a) A segment of a (ProProGly)10 triple helix. (b) Comparison of the stability ofa triple helix formed from (ProProGly)4–ProProOGly–(ProProGly)5, whereinone Pro–Gly amide bond is replaced with an ester, with that in panel a revealingthat each interstrand hydrogen bond contributes �G = −2.0 kcal/mol totriple-helix stability (30). (c) Crystal structure of a triple helix formed from acollagen-related peptide that mimics a common sequence in type IV collagen,(GlyProHyp)3–(3S-HypHypGly)2–(GlyProHyp)4, showing that 3S-Hyp in theXaa position yields a prototypical collagen triple helix [PDB entry 2g66 (78)].(d ) (2S,3S )-3-Fluoroproline in the Xaa position destabilizes a collagen triplehelix, perhaps by withdrawing electron density from the proximal Xaa carbonyland thereby reducing the strength of the interstrand hydrogen bond (79).

OI: osteogenesisimperfecta

acid replacing Gly and the location of that sub-stitution can impact the pathology of, for ex-ample, osteogenesis imperfecta (OI) (33, 36).Substitutions for Gly in proline-rich portionsof the collagen sequence (Figure 3a) are far lessdisruptive than those in proline-poor regions, atestament to the importance of Pro derivativesfor triple-helix nucleation (37). In vivo, triplehelices fold in a C-terminal→N-terminal man-ner (38). The time delay between disruption oftriple-helix folding by a Gly substitution andrenucleation of the folding process N-terminalto the substitution site is much shorter when


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Protocollagen: thenonhydroxylated,nontriple-helical formof collagen prior to theaction of P4H, P3H,lysyl hydroxylase, andprotein disulfideisomerase

Preorganization: theextent to which hostsand guests areorganized for bindingprior to theircomplexation, therebyincreasing complexstability

P4H: prolyl4-hydroxylase

triple-helix nucleating, proline-rich sequencesare immediately N-terminal to the substitutionsite (37). Any delay in triple-helix folding resultsin overmodification of the protocollagen chains[in particular, inordinate hydroxylation of Lysresidues N-terminal to the Gly substitution andexcessive glycosylation of the resultant hydrox-ylysine residues (Figure 2)], thereby perturb-ing triple-helical structure and contributing tothe severity of OI (39). Thus, the severity ofOI correlates with the abundance of triple-helixnucleating, proline-rich sequences immediatelyN-terminal to the substitution site (36).

Prolines in the Xaa and Yaa Positions

In the strands of human collagen, ∼22% of allresidues are either Pro or Hyp (9). The abun-dance of these residues preorganizes the indi-vidual strands in a PPII conformation, therebydecreasing the entropic cost for collagen fold-ing (40). Despite their stabilizing properties,Pro derivatives also have certain deleteriousconsequences for triple-helix folding and sta-bility that partially offset their favorable effects.For example, Pro has a secondary amino groupand forms tertiary amides within a peptide orprotein. Tertiary amides have a significant pop-ulation of both the trans and the cis isomers(Figure 5), whereas all peptide bonds in col-lagen are trans. Thus, before a (ProHypGly)n

strand can fold into a triple helix, all the cis

NO

O

Ktrans/cis

transcis

NO

O

Figure 5Pro cis-trans isomerization. Unlike otherproteinogenic amino acids, Pro forms tertiary amidebonds, resulting in a significant population of the cisconformation.

peptide bonds must isomerize to trans. N-Methylalanine (an acyclic, tertiary amide miss-ing only Cγ of Pro) decreases triple-helix stabil-ity when used to replace Pro or Hyp in CRPs,presumably because it lacks the preorganizationimposed by the pyrrolidine ring of Pro deriva-tives (41). In contrast, avoiding the issue of cis-trans isomerization altogether by replacing aGly–Pro amide bond with a trans-locked alkeneisostere also results in a destabilized triple helix,despite leaving all interchain hydrogen bondsintact (42). Clearly, the factors dictating triple-helix structure and stability are intertwined in acomplex manner (vide infra).

Pro residues in the Yaa position of pro-tocollagen triplets are modified by prolyl 4-hydroxylase (P4H), a nonheme iron enzymethat catalyzes the posttranslational and stere-oselective hydroxylation of the unactivatedγ-carbon of Pro residues in the Yaa positionof collagen sequences to form Hyp (Figure 6).P4H activity is required for the viability of

P4HFe(II)

O2

CO2

CO2–

O

–O2C

–ProProGly– –ProHypGly–

N

HN

O

O

ON

HH

N

HN

O

O

ON

HOH

O

O––O2C

Figure 6Reaction catalyzed by prolyl 4-hydroxylase (P4H). Pro residues in the Yaa position of collagen strands areconverted into Hyp prior to triple-helix formation.


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both the nematode Caenorhabditis elegans andthe mouse Mus musculus (43, 44). Thus, Hyp isessential for the formation of sound collagen invivo.

Role of Hyp

The hydroxylation of Pro residues in the Yaaposition of collagen increases dramatically thethermal stability of triple helices (Table 2).This stabilization occurs when the resultantHyp is in the Yaa position (45, 46) but notin the Xaa position, nor when the hydroxyl

Table 2 Values of Tm for triple-helical CRPs

(XaaYaaGly)n Tm (◦C)a References(ProFlpGly)7 45 (54)(ProHypGly)7 36 (54)(mepMepGly)7 36 (65)(flpProGly)7 33 (68)(ProMepGly)7 29 (65)(ProClpGly)7 23 (61)(mepProGly)7 13 (65)(clpProGly)7 No helix (61)(ProProGly)7 No helix (79)(flpFlpGly)7 No helix (79)(ProflpGly)7 No helix (54)(FlpProGly)7 No helix (68)(ProFlpGly)10 91 (53)(ProMopGly)10 70 (59)(HypHypGly)10 65 (85)(ProHypGly)10 61–69 (53, 85)(flpProGly)10 58 (69)(ProClpGly)10 52 (61)(clpProGly)10 33 (61)(ProProGly)10 31–41 (53, 64)(flpFlpGly)10 30 (94)(clpClpGly)10 No helix (61)(HypProGly)10 No helix (84)(ProhypGly)10 No helix (47)(FlpProGly)10 No helix (69)(ClpProGly)10 No helix (61)(hypProGly)10 No helix (47)

aValues of Tm depend on both CRP concentration andheating rate. Hence, detailed comparisons requireknowledge of experimental procedures.

hyp: (2S,4S )-4-hydroxyproline

Flp: (2S,4R)-4-fluoroproline

flp: (2S,4S )-4-fluoroproline

Stereoelectroniceffects: relationshipsbetween structure,conformation, energy,and reactivity thatresult from thealignment of filled orunfilled electronicorbitals

group is installed in the 4S configuration as in(2S,4S )-4-hydroxyproline (hyp) (Table 2) (47,48). These findings led to the proposal that the4R configuration of a prolyl hydroxyl group isprivileged in alone enabling the formation ofwater-mediated hydrogen bonds that stitch to-gether the folded triple helix (49). Indeed, suchwater bridges between Hyp and main chainheteroatoms were observed by Berman andcoworkers (19, 50) in their seminal X-ray crys-tallographic studies of CRPs. The frequency ofHyp in most natural collagen is, however, toolow to support an extensive network of waterbridges. For example, four or more repeatingtriads of Xaa–Hyp–Gly occur only twice in theamino acid sequence of human type I collagen.

The hypothesis that the water bridgesobserved in crystalline (ProHypGly)n triplehelices are meaningful was tested by replacingHyp residues in CRPs with (2S,4R)-4-fluoroproline (Flp). As fluoro groups do notform strong hydrogen bonds (51), waterbridges cannot play a major role in stabilizinga (ProFlpGly)10 triple helix. Nonetheless,(ProFlpGly)10 triple helices are hyperstable(Table 2) (52, 53). Accordingly, water bridgescannot be of fundamental importance fortriple-helix stability. How, then, does 4R-hydroxylation of Yaa-position Pro residuesstabilize the triple helix?

A gauche effect. Replacing Hyp in the Yaaposition with (2S,4S )-4-fluoroproline (flp),a diastereomer of Flp, prevents triple-helixformation (Table 2) (54). This discoverythat the stereochemistry of electronegativesubstituents at the 4-position of the Pro ringis important for the formation of stable triplehelices suggests that Flp and Hyp in the Yaaposition stabilize collagen via a stereoelectroniceffect, rather than a simple inductive effect(54). Pro and its derivatives prefer one of twomajor pyrrolidine ring puckers, which aretermed Cγ-exo and Cγ-endo (Figure 7). [Thering actually prefers two distinct twist, ratherthan envelope, conformations (55). As Cγ

experiences a large out-of-plane displacementin the twisted rings, we refer to pyrrolidine ring


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NO

R2

R1

NO

R2

R1

Cγ-endo pucker Cγ-exo pucker

Figure 7Ring conformations of Pro and Pro derivatives. TheCγ-endo conformation is favored strongly bystereoelectronic effects when R1 = H, R2 = F (flp) orCl (clp), and by steric effects when R1 = Me (mep)or SH (mcp), R2 = H. The Cγ-exo conformation isfavored strongly by stereoelectronic effects whenR1 = OH (Hyp), F (Flp), OMe (Mop), or Cl (Clp),R2 = H, and by steric effects when R1 = H, R2 = Me(Mep) or SH (Mcp). The Cγ-endo:Cγ-exo ratio is ∼2when R1 = R2 = H (56).

puckers simply as Cγ-exo and Cγ-endo.] Proitself has a slight preference for the Cγ-endoring pucker (Table 3) (56). A key attributeof a 4R fluoro group on Pro (as well as thenatural 4R hydroxyl group) is its impositionof a Cγ-exo pucker on the pyrrolidine ringvia the gauche effect (Figure 8a,b) (56–58).The Cγ-exo ring pucker preorganizes the mainchain torsion angles (φ, C′

i−1–Ni–Cαi–C′

i; ψ ,Ni–Cα

i–C′i–Ni+1; and ω, Cα

i–C′i–Ni+1–

Cαi+1) to those in the Yaa position of a triplehelix (Table 4). Thus, 4R-hydroxylation ofPro residues in the Yaa position of collagenstabilizes the triple helix via a stereoelectroniceffect. Flp is more stabilizing than Hyp becausefluorine (χF = 4.0) is more electronegativethan oxygen (χO = 3.5), and a fluoro group

Table 3 Conformation of Pro and its 4-substituted derivatives that prefer the Xaa position [φ = −75◦, ψ = 164◦ (7)] in acollagen triple helix

Residue(References)

Crystal structure

Ringpucker

(Eendo–Eexo)a (kcal/mol)

ϕ(degrees)

ψ(degrees)

Pro (54, 56, 57) –0.41 –79b

–76b

177b 4.6

mcp (66) — 4.7

mep (65) — –1.4

flp (54, 56, 68) — –0.61 172a 2.5

clp (61) — —

— —

—

—

—

aFrom DFT calculations. bValues of ϕ and ψ (here, Ni–Cα

i–C’i–Oi+1) are from the crystal structure of Ac-Pro-OMe, which has a cis peptide bond.cValues of Ktrans/cis (Figure 5) were determined in solution by NMR spectroscopy.

Ktrans/cisc

Cγ-endo

Cγ-endo

Cγ-endo

Cγ-endo

Cγ-endo 2.2——

3.7


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(FF = 0.45) manifests a greater inductive effectthan does a hydroxyl group (FOH = 0.33).Thus, a 4R fluoro group enforces the Cγ-exoring pucker of a Pro derivative more stronglythan does a 4R hydroxyl group.

To probe further the role of Hyp in collagenstability, a (2S,4R)-4-methoxyproline residue(Mop) was incorporated into the Yaa positionof a (ProYaaGly)10 CRP (59). O-Methylationis perhaps the simplest possible covalent mod-ification of a Hyp residue and reduces the ex-tent of hydration without altering significantlythe electron-withdrawing ability of the 4R sub-stituent. Accordingly, Mop and Hyp residueshave similar conformations (Table 4). Interest-ingly, reducing the hydration of (ProHypGly)10

by methylation of Hyp residues enhances triple-helix stability significantly (Table 2). Moreover,alkylation with functional groups larger thana methyl group does not necessarily perturbtriple-helix stability (60). Notably, (2S,4R)-4-chloroproline (Clp) residues also stabilize triplehelices in the Yaa position (Table 2) (61). LikeFlp, Clp has a strong preference for the Cγ-exoring pucker, and a (ProClpGly)10 triple helixis therefore more stable than a (ProProGly)10

triple helix. Thus, a plethora of data indicatethat the hydroxyl group of Hyp stabilizes col-lagen through a stereoelectronic effect. Waterbridges provide little (if any) net thermody-namic advantage to natural collagen (59).

Surprisingly, a host-guest CRP of theform AcGly–(ProHypGly)3–ProFlpGly–(ProHypGly)4–GlyNH2 actually forms a less stabletriple helix than does AcGly–(ProHypGly)8–GlyNH2 (62). In contrast, a host-guest CRPof the form (GlyProHyp)3–GlyProFlp–GlyValCys–GlyAspLys–GlyAsnPro–GlyTrpPro–GlyAlaPro–(GlyProHyp)4-NH2 forms a morestable triple helix than one containing Hyprather than Flp (63). These results suggest thata fluoro group might disrupt the hydrationinduced by a long string of Hyp residues.Kobayashi and coworkers (64) used differentialscanning calorimetry to demonstrate that(ProHypGly)10 triple helices are stabilized byenthalpy, whereas (ProFlpGly)10 triple helicesare stabilized by entropy. These findings are

Stereoelectroniceffects

Gaucheeffect

Cγ-exopucker

HighKtrans/cis

a

H

N HR1=EWG

HO

N

H

HR1=EWG

HOb

Gauche conformationCγ-exo pucker

c

Anti conformationCγ-endo pucker

NO

O

R1R2

n→ *interaction

π

Consequentpreorganization

Stabletriplehelix

d

Figure 8Stereoelectronic effects that stabilize the collagen triple helix. (a) A gaucheeffect and an n→π∗ interaction preorganize main chain torsion angles andenhance triple-helix stability. (b) A gauche effect, elicited by an electron-withdrawing group (EWG) in the 4R position, stabilizes the Cγ-exo ringpucker. (c) An n→π∗ interaction stabilizes the trans isomer of the peptide bondbut is substantial only when Pro derivatives are in the Cγ-exo ring pucker (e.g.,R1 = OH or F, R2 = H). (d ) Depiction of overlap between n and π∗ naturalbond orbitals (NBOView c©) in a Pro residue with Cγ-exo pucker.

consistent with Hyp decreasing the entropiccost for folding via main chain preorganizationbut increasing that cost by specific hydration.This interpretation is in accord with the sta-bility of (ProMopGly)10 triple helices arisingfrom a nearly equal contribution of enthalpyand entropy (59).

A steric effect. Electronegative substituentson Pro rings are not the only means of en-forcing an advantageous ring pucker. Pro ringpucker can also be dictated by steric effects,as in (2S,4S )-4-methylproline (Mep) (65) and(2S,4R)-4-mercaptoproline (Mpc) (Figure 7)(66). The 4-methyl substituent of Mep prefersthe pseudoequatorial orientation and thusenforces the Cγ-exo ring pucker of Pro (analo-gous results are observed for Mpc) (Table 4).


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Table 4 Conformation of 4-substituted derivatives of Pro that prefer the Yaa position [φ = −60◦, ψ = 152◦ (7)] in acollagen triple helix

Residue(References)

Crystal structure

Ringpucker

(Eendo–Eexo)a (kcal/mol)

ϕb

(degrees)ψb

(degrees)

Mep (65) 1.7 –62d

–58

–55

–57

153d

148

141

7.4

Mop (59) 6.7

Flp (52, 54, 56, 57) 0.85

Hyp (46, 54, 57, 58) 151

148

6.1

Clp (61)

Mcp (66) —

—

— — —

—

—

aFrom DFT calculations. bValues of ϕ and ψ (here, Ni–Cα

i–C’i–Oi+1) are from the crystal structure of Ac-Yaa-OMe.cValues of Ktrans/cis (Figure 5) were determined in solution by NMR spectroscopy. dM.D. Shoulders, I.A. Guzei & R.T. Raines, unpublished data.

Ktrans/cisc

Cγ-exo

Cγ-exo

Cγ-exo

Cγ-exo

Cγ-exo

Cγ-exo

5.4

5.4

–56

6.7

Indeed, triple helices formed from(ProMepGly)7 have stability similar tothose formed from (ProHypGly)7 (Table 2)(65).

Proline Derivatives in the Xaa Position

The Cγ-exo ring pucker of Pro residues inthe Yaa position enhances triple-helix stability.Likewise, the ring pucker of Pro in the Xaa posi-tion is important for triple-helix stability. Typi-cally, Pro residues in the Xaa position of biolog-ical collagen are not hydroxylated and usuallydisplay the Cγ-endo ring pucker (67). By em-ploying Cγ-substituents, both the gauche effectand steric effects can be availed to preorganize

the Cγ-endo ring pucker (Figures 7 and 8). In-stallation of flp, (2S,4S )-4-chloroproline (clp),or (2S,4R)-4-methylproline (mep) residues (allof which prefer the Cγ-endo ring pucker)(Table 3) in the Xaa position of collagen isstabilizing relative to Pro, but installation ofFlp, Clp, or Hyp (which prefer the Cγ-exo ringpucker) is destabilizing (Table 2) (61, 65, 68–70). These results suggest that preorganizingthe Cγ-endo ring pucker in the Xaa position ofCRPs stabilizes triple helices. This conclusionis reasonable because Pro derivatives with a Cγ-endo ring pucker have φ and ψ main chain tor-sion angles similar to those observed in the Xaaposition of triple helices (Table 3).


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Notably, replacing Pro in the Xaa position of(ProProGly)10 with hyp, a Pro derivative that,like flp and clp, should prefer the Cγ-endo ringpucker owing to the gauche effect, yields CRPsthat do not form triple helices (Table 2) (47).This anomalous result for hyp in the Xaa posi-tion could be attributable to deleterious hydra-tion, idiosyncratic conformational preferencesof hyp residues, or both (71).

Type IV collagen, which is the primary com-ponent of basement membranes, has a high in-cidence of (2S,3S )-3-hydroxyproline (3S-Hyp)in the Xaa position (72). This modification ispresent in some other collagen types and in in-vertebrate collagens. 3S-Hyp, which prefers aCγ-endo ring pucker (73), is introduced almostexclusively within ProHypGly triplets via post-translational modification of individual colla-gen strands by prolyl 3-hydroxylase (P3H),which is distinct from P4H (74). A recessiveform of OI is associated with a P3H defi-ciency (75, 76). Certain mutations to the geneencoding cartilage-associated protein, a P3H-helper protein, prevent 3S-hydroxylation ofα1(I)Pro986 as well as 3S-hydroxylation ofsome other Xaa-position Pro residues, result-ing in a phenotype nearly identical to clas-sical OI. The underlying basis for the im-portance of 3S-hydroxylation of α1(I)Pro986is unclear but could involve lower rates oftriple-helix secretion (76). Replacing Pro with3S-Hyp in the Xaa position of CRPs can en-hance triple-helix stability slightly (73, 77). Acrystal structure of a triple helix containing3S-Hyp substitutions reveals the maintenanceof the prototypical triple-helix structure andthe absence of unfavorable steric interactions(Figure 4c) (78). In contrast, replacing 3S-Hyp with (2S,3S )-3-fluoroproline destabilizesa triple helix markedly, possibly owing to athrough-bond inductive effect that diminishesthe ability of its main chain oxygen to accept ahydrogen bond (Figure 4d ) (79).

An n→π∗ Interaction

A general principle in the design of CRPsis that Pro residues with either a Cγ-endo or

Cγ-exo ring pucker will stabilize triple he-lices in the Xaa and Yaa positions, respectively(Tables 2–4). Appropriate ring pucker, en-forced by a stereoelectronic or steric effect, pre-organizes the φ and ψ torsion angles to thoserequired for triple-helix formation.

Intriguingly, the stability of a (flpProGly)7

or (clpProGly)10 triple helix is significantly lessthan that of a (ProFlpGly)7 or (ProClpGly)10

triple helix, respectively (Table 2) (61, 68).Likewise, a (mepProGly)7 triple helix isless stable than a (ProMepGly)7 triple helix(Table 2) (65). Two factors contribute to thelower stability of triple helices formed fromCRPs with stabilizing Pro derivatives substi-tuted in the Xaa position rather than the Yaaposition. First, a Cγ-endo ring pucker is alreadyfavored in Pro (56); flp, clp, and mep merelyenhance that preference (Table 3). In contrast,Flp, Clp, Hyp, and Mep have the more dramaticeffect of reversing the preferred ring pucker ofPro, thereby alleviating the entropic penaltyfor triple-helix formation to a greater extent(Table 4). Second, Flp, Clp, and Mep in theYaa position cause favorable preorganization ofall three main chain torsion angles (φ, ψ , andω) (Table 4). In contrast, flp, clp, and mep havea low probability of adopting a trans peptidebond (ω = 180◦) (54, 61, 65) relative to Pro(Table 3), thereby mitigating the benefit ac-crued from proper preorganization of φ and ψ .Notably, 13C-NMR studies on collagen in vitroshow that 16% of Gly–Pro bonds in unfoldedcollagen are in the cis conformation, whereasonly 8% of Xaa–Hyp bonds in unfolded col-lagen are cis, an observation that confirms theeffect of Cγ-substitution on the conformationof the preceding peptide bond (80).

How does the effect of a 4-X substituenton Pro ring pucker influence the peptide bondisomerization equilibrium constant (Ktrans/cis)(Figure 5 and Tables 3 and 4)? The ex-planation stems from another stereoelectroniceffect: an n→π∗ interaction (56, 81). In ann→π∗ interaction, the oxygen of a peptide bond(Oi−1) donates electron density from its lonepairs into the antibonding orbital of the car-bonyl in the subsequent peptide bond (Ci

′==Oi)


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(Figure 8c,d ). The Cγ-exo ring pucker ofa Pro residue provides a more favorableOi−1. . .Ci

′==Oi distance and angle for an n→π∗

interaction than does the Cγ-endo pucker (56).Importantly, Ktrans/cis for peptidyl prolyl amidebonds is determined by the pyrrolidine ringpucker and is not generally affected by theidentity of substituents in the 4-position of thepyrrolidine ring (82). Because an n→π∗ interac-tion can occur only if the peptide bond contain-ing Oi−1 is trans, the n→π∗ interaction has animpact on the value of Ktrans/cis for main chainswith appropriate torsion angles (Table 4).Thus, imposing a Cγ-exo pucker on a pyrroli-dine ring in the Yaa position of a CRP preorga-nizes not only the φ and ψ angles for triple-helixformation, but also the ω angle. Indeed, a singlen→π∗ interaction can stabilize the trans confor-mation by �G◦ = −0.7 kcal/mol (81, 83).

Hyp in the Xaa Position

In the Xaa position, a Pro residue with a Cγ-endo pucker generally stabilizes a triple helix,whereas one with a Cγ-exo pucker destabilizes atriple helix. For example, (HypProGly)n triplehelices are far less stable than (ProProGly)n

triple helices (Table 2) (84) because Hypprefers the Cγ-exo ring pucker and thus preor-ganizes the φ and ψ torsion angles improperlyfor the Xaa position of a collagen triple helix(Table 4). Surprisingly, (HypHypGly)10 triplehelices are actually slightly more stable than(ProHypGly)10 triple helices (Table 2) (85, 86)despite the Hyp residues in the Xaa positionof (HypHypGly)10 displaying the Cγ-exo ringpucker in the triple helix (87, 88). It is notewor-thy that crystal structures of (HypHypGly)10

show that the main chain torsion angles in theXaa position of a (HypHypGly)n triple helix ad-just to accommodate a Cγ-exo ring pucker inthat position (87, 88).

The finding that Hyp can stabilize triple he-lices in the Xaa position in a context-dependentmanner was presaged in a study by Gruskinand coworkers (89) on the global substitutionof Hyp for Pro in recombinant type I col-lagen polypeptides that formed stable triple

helices. Notably, Hyp is found in the Xaaposition of some invertebrate collagens (90)and can be acceptable in CRPs in which theYaa position residue is not Pro (86, 91, 92).Berisio and coworkers (93) have suggested that(HypHypGly)10 triple helices might be hyper-stable owing to interstrand dipole-dipole in-teractions between proximal Cγ–OH bonds ofadjacent Hyp residues. Kobayashi and cowork-ers (87) have proposed that the stability of(HypHypGly)10 triple helices is attributable tothe high hydration level of the peptide chainsin the single-coil state prior to triple-helix for-mation, which could reduce the entropic costof water bridge formation. A combination ofthese factors is likely to be responsible for thisanomaly.

Heterotrimeric SyntheticTriple Helices

Both flp and Flp greatly enhance triple-helixstability when in the Xaa and Yaa position,respectively. Nonetheless, (flpFlpGly)n formsmuch less stable triple helices than does(ProProGly)n (Table 2) (79, 94). In such ahelix, the fluorine atoms of flp and Flp residuesin alternating strands would be proximal, andthe C–F dipoles would interact unfavorably(Figure 9a) (79). These negative steric andelectronic interactions presumably compro-mise triple-helix stability despite appropriatepreorganization of main chain torsion angles.This hypothesis was confirmed by two otherfindings. First, a (clpClpGly)10 triple helix doesnot even form at 4◦C, whereas a (flpFlpGly)10

triple helix has Tm = 30◦C (Table 2) (61, 94).The steric clash between chlorine atoms ofopposing clp and Clp residues is exacerbatedby the large size of chlorine relative to fluo-rine (Figure 9b). Second, (mepMepGly)7

forms more stable triple helices than doeither of the corresponding mono-substitutedCRPs, (mepProGly)7 and (ProMepGly)7

(Table 2). The 4-methyl groups protrude radi-ally from the triple helix (Figure 9c) and thuscannot interact detrimentally with each other(65).


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a b c

d

flpFlp

clpClp

mep Mep

Unstable

Stable

(ProHypGly)10: neutral strand

(AspHypGly)10: anionic strand

(ProLysGly)10: cationic strand

+

+

Figure 9Heterotrimeric synthetic collagen triple helices. (a–c) Steric approach. Space-filling models of triple-helixsegments constructed from the structure of a (ProHypGly)n triple helix [PDB entry 1cag (19)] with theprogram SYBYL (Tripos, St. Louis, MO). In panel a, rF···F = 2.4 A in a (flpFlpGly)n triple helix (79). In panelb, rCl···Cl = 1.9 A (61) in a (clpClpGly)n triple helix. In panel c, the methyl groups in a (mepMepGly)n triplehelix are radial and distal. (d ) Coulombic approach. Favorable Coulombic interactions drive the preferentialassembly of triple helices having a 1:1:1 ratio of (ProLysGly)10:(AspHypGly)10:(ProHypGly)10 (96).

The steric and stereoelectronic effectson triple-helix stability manifested in the(flpFlpGly)7 CRP provided, for the first time, ameans to generate noncovalently linked, het-erotrimeric triple helices with defined stoi-chiometry. Analysis of triple-helix cross sec-tions suggested a triple helix composed of(flpFlpGly)7:(ProProGly)7 in either a 1:2 or2:1 ratio could be stable, as the presenceof some Pro residues in the Xaa and Yaapositions would eliminate deleterious stericinteractions between fluorine residues in op-posing strands. A (flpFlpGly)7:(ProProGly)7

ratio of 2:1 yielded the most stable triple he-lices, thereby demonstrating the first instance of

heterotrimeric assembly of triple helices withcontrolled stoichiometry (79) and suggestingthe possibility of developing a “code” for triple-helix assembly along the lines of the Watson-Crick code for DNA assembly.

Gauba & Hartgerink (95) developedan alternative strategy that employsCoulombic interactions to guide the as-sembly of heterotrimeric triple helices.They observed that a 1:1:1 mixture of(ProArgGly)10:(GluHypGly)10:(ProHypGly)10

produces triple helices containing one neg-atively charged, one positively charged, andone neutral CRP. Intriguingly, a (ProLysGly)10:(AspHypGly)10:(ProHypGly)10 triple helix has


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Self-assembly: aprocess in whichspecific, localinteractions betweendisorderedcomponents lead to anorganized structure,without externaldirection

Collagenfibrillogenesis: theprocess oftropocollagenmonomers assemblinginto mature fibrils

a Tm value similar to that of a (ProHypGly)10

homotrimer, even though Asp and Lys areknown to destabilize significantly the triplehelix relative to Pro and Hyp (Figure 9d ). Thisfinding demonstrates the utility of Coulom-bic interactions for stabilizing triple helices(96).

Synthetic collagen heterotrimers are appeal-ing mimics of natural collagen strands, as mostcollagen types are themselves heterotrimers(Table 1). Gauba & Hartgerink (97) employedtheir Coulombic approach to generate mim-ics of type I collagen variants that lead to OI.Specifically, they studied the stability of triple-helical heterotrimers containing one, two, orthree Gly→Ser substitutions. They observedthat a Gly→Ser substitution in only one or twochains is not as debilitating for triple-helix sta-bility and folding as is a Gly→Ser substitutionin all three chains.

AVOIDING AGGREGATION

Long, unfolded polypeptides have an innate tendency to formaggregates (145), such as the amyloid fibrils implicated in neu-rodegenerative diseases. Interestingly, despite their long lengthand slow folding, protocollagen strands are not known to aggre-gate. Amyloid fibrils and other aggregates are composed largelyof β-sheets (146). Pro and Gly are the two amino acid residueswith the lowest propensity to form a β-sheet (147, 148), and Glyresidues are known explicitly to reduce protein aggregation rates(149).

We propose that the prevalence of Pro and Gly residues inprotocollagen is necessary to avert the formation of harmful ag-gregates. This proposal is supported by the remarkably highPro/Gly content of other fibrous, structural proteins in plantsand animals, such as elastin, extensin, glycine-rich proteins, andproline-rich proteins. Molecular dynamics simulations of elastinpolypeptides likewise support this proposal, as a minimum thresh-old of Pro/Gly content must be attained to realize elastomers in-stead of amyloid fibrils (150). Apparently, the molecular evolutionof collagen and other fibrous, structural proteins has availed Proand Gly residues to avoid β-sheet formation and the consequentformation of harmful aggregates.

Nonproline Substitutions in the Xaaand Yaa Positions

Brodsky and coworkers (9) determined thefrequency of occurrence of all possible tripep-tides in a set of fibrillar and nonfibrillar col-lagen sequences. Only a few of the 400 possi-ble triplets formed from the 20 natural aminoacids are observed with any frequency in col-lagen. Additionally, they have examined ex-haustively the incorporation of all 20 commonamino acids in the Xaa and Yaa positions ofCRPs using a host-guest model system whereina single XaaYaaGly triplet is placed withina (ProProGly)n or (ProHypGly)n CRP (98).These host-guest studies revealed a correlationbetween the propensity of a particular residue toadopt a PPII conformation and its contributionto triple-helix stability (98). Notably, Arg in theYaa position confers triple-helix stability similarto Hyp (99). The aromatic amino acid residuesTrp, Phe, and Tyr are all strongly destabilizingto the triple helix (98), although the structuralbasis for this destabilization is unclear. Brodskyand coworkers (100) used their data on host-guest CRPs to develop an algorithm that en-ables a priori calculation of the effect of Xaaand Yaa substitutions on triple-helix stability.

HIGHER-ORDER COLLAGENSTRUCTURE

In vivo collagen has a hierarchical struc-ture (Figure 2). Individual TC monomersself-assemble into the macromolecular fibersthat are essential components of tissues andbones. The self-assembly processes involved incollagen fibrillogenesis are of enormous impor-tance to ECM pathology and proper animal de-velopment (see the sidebar “Avoiding Aggre-gation” for a discussion of how collagen self-assembly might be directed away from delete-rious protein aggregates).

Fibril Structure

There are many classes of collagenous struc-tures in the ECM, including fibrils, networks,


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and transmembrane collagenous domains. Forbrevity, we focus here on fibrils composed pri-marily of type I collagen.

TC monomers of type I collagen have theunique property of actually being unstable atbody temperature (101); that is, the random coilconformation is the preferred one. How can sta-ble tissue structures form from an unstable pro-tein? The answer must be that collagen fibrillo-genesis has a stabilizing effect on triple helices.Moreover, the assembly of strong macromolec-ular structures is essential to enable collagen tosupport stress in one, two, and three dimensions(102). The importance of collagen fibrillogen-esis is underscored by the conclusion of Kadlerand coworkers (103) that the fundamental prin-ciples underlying the formation of some typesof modern collagen fibrils were established atleast 500 Mya.

Collagen fibrillogenesis in situ occurs via as-sembly of intermediate-sized fibril segments,called microfibrils (Figure 2) (104). Thus, thereare two important issues for understandingthe molecular structure of the collagen fibril.First, what is the arrangement of individual TCmonomers within the microfibril? Second, whatis the arrangement of the individual microfib-rils within the collagen fibril? These questionshave proven difficult to answer, as individualnatural microfibrils are not isolable and thelarge size and insolubility of mature collagenfibrils prevent the use of standard structure-determination techniques.

Collagen fibrils formed mainly from typeI collagen (all fibrous tissues except cartilage)and fibrils formed largely from type II collagen(cartilage) have slightly different structures. Al-though we focus solely on type I collagen fib-rils, recent data have enabled the determinationof thin cartilage fibril structure to intermedi-ate resolution (∼4 nm). This structure suggeststhat cartilage collagen fibrils have a 10 + 4 het-erotypic microfibril structure—meaning thatthe fibril surface presents ten equally spaced mi-crofibrils and that there are four equally spacedmicrofibrils in the core of the fibril (105).

Fibrils of type I collagen in tendon are upto 1 cm in length (106) and up to ∼500 nm

D-Periodicity: theaxial stagger ofadjacent tropocollagenmolecules by adistance, D, which isthe sum of gap andoverlap regions

in diameter. An individual triple helix in typeI collagen is <2 nm in diameter and ∼300 nmlong. Clearly, fibrillogenesis on an extraordi-nary scale is necessary to achieve the structuraldimensions of natural collagen fibrils. The mostcharacteristic feature of collagen fibrils is thatthey are D-periodic with D = 67 nm. Thebanded structure observed in transmission elec-tron microscopy (TEM) images of collagen fib-rils occurs because the actual length of a TCmonomer is not an exact multiple of D butL = 4.46D, resulting in gaps of 0.54D and over-laps of 0.46D (Figure 2). This regular array ofgap and overlap regions must be accounted forin structural models of the collagen fibril andmicrofibril.

The initial proposal for the three-dimensional structure of fibrillar collagenwas a simplified structural model for collagenmicrofibrils advanced by Hodge & Petruska(107) in 1963. Their model consists of a two-dimensional stack in which five TC monomerswithin a microfibril are offset by D = 67 nmbetween neighboring strands (Figure 2). Thismodel accounts for the gap and overlap regionsapparent in mature collagen fibrils by TEMand atomic force microscopy (AFM). Manyresearch groups began efforts to determine thethree-dimensional structure of type I collagenfibrils at higher resolution. Numerous modelswere proposed to account for the featuresof fiber diffraction and of TEM and AFMimages of such fibrils (108–111). Researchersgenerally agreed on a quasi-hexagonal unitcell containing five TC monomers as the basisfor an accurate model of the collagen fibril,but important details were in dispute. Recentfindings indicate that the fibril structurecontroversy is approaching resolution.

In 2001, Orgel and coworkers (112, 113)reported the first electron-density map of atype I collagen fiber at molecular anisotropicresolution (axial: 5.16 A; lateral: 11.1 A) us-ing synchrotron radiation. Their data con-firm that collagen microfibrils have a quasi-hexagonal unit cell. The molecular packing ofthe TC monomers in this model results inTC neighbors arranged to form supertwisted,


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Collagentelopeptides: N- andC-terminal 11- to26-residuenontriple-helicaldomains oftropocollagen strandsinvolved infibrillogenesis andcross-linking

Procollagen: thehydroxylated form ofcollagen prior tocollagen propeptidecleavage

Collagenpropeptides: N- andC-terminalnontriple-helicaldomains of collagenstrands that directtriple-helix foldingprior to fibrillogenesis

right-handed microfibrils that interdigitatewith neighboring microfibrils—leading to aspiral-like structure for the mature collagen fib-ril (113). Their model advances the provoca-tive idea that the collagen fibril is a networked,nanoscale rope—an idea also suggested by theAFM studies of Bozec and coworkers (111).

Orgel and coworkers determined the axiallocation of the N- and C-terminal collagentelopeptides and found that neighboringtelopeptides within a TC monomer interactwith each other and are cross-linked covalentlysubsequent to the action of lysyl oxidase(114). The cross-links can be both within andbetween microfibers. Intriguingly, the super-twisted nature of the collagen microfibril ismaintained through the nonhelical telopeptideregions (113).

This new model of the fibril of type I colla-gen explains the failure of previous researchersto isolate individual collagen microfibrils fromtissue samples: The microfibrils interdigitateand cross-link, thus preventing separation fromeach other in an intact form. The new modelalso justifies the observation that TC in fib-rils is far more resistant to collagen proteolysisby matrix metalloproteinase 1 (MMP1) than ismonomeric TC; the collagen fibril protects re-gions vulnerable to proteolysis by MMP1. Pro-teolysis of the C-terminal telopeptide of TCin a fibril is required before MMP1 can gainaccess to the cleavage site of a TC monomer(115).

Nucleation and Modulationof Collagen Fibrillogenesis

Collagen fibrillogenesis requires completionof two stages of self-assembly: nucleation andfiber growth. Collagen fibrillogenesis beginsonly after procollagen N- and C-proteinasescleave the collagen propeptides at each triple-helix terminus to generate TC monomers. TheC-terminal propeptides are essential for propertriple-helix formation but prevent fibrilloge-nesis (116). After cleavage of the propeptides,TC monomers are composed of a lengthytriple-helical domain consisting of a repeating

XaaYaaGly sequence flanked by short,nontriple-helical telopeptides (Figure 2).

The C-terminal telopeptides of TC areimportant for initiating proper fibrillogenesis.Prockop and Fertala (117) suggested that colla-gen self-assembly into fibrils is driven by the in-teraction of C-terminal telopeptides with spe-cific binding sites on triple-helical monomers.The addition of synthetic telopeptide mimicscan inhibit collagen fibrillogenesis, presumablyby preventing the interaction between collagentelopeptides and TC monomers. Triple heliceslacking the telopeptides can, however, assem-ble into fibrils with proper morphology (118).Thus, collagen telopeptides could acceleratefibril assembly and establish the proper regis-ter within microfibrils and fibrils but might notbe essential for fibrillogenesis.

Collagen telopeptides have a second rolein stabilizing mature collagen fibrils. Lys sidechains in the telopeptides are cross-linked sub-sequent to fibril assembly, forming desmosineand isodesmosine cross-links between Lys andhydroxylysine residues with the aid of lysyloxidase (Figure 2) (119). The cross-linkingprocess endows mature collagen fibrils withstrength and stability, but is not involved in fib-rillogenesis. Thus, although collagen telopep-tides might not be essential for nucleatingcollagen fibrillogenesis, their absence greatlyweakens the mature fibril owing to the lack ofcross-links within and between triple helices(119).

MECHANICAL PROPERTIESOF COLLAGEN FIBRILS

The hierarchical nature of collagen structuretheoretically enables evaluation of the me-chanical properties of collagen at varying lev-els of structural complexity, including the TCmonomer, individual collagen fibrils, and col-lagen fibers. Perhaps the most direct measuresof the mechanical properties of collagen havebeen obtained by studying TC monomers andfibrils formed from type I collagen. Researchershave employed various biophysical and theo-retical techniques over the past 20 years, and


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recent advances in AFM methodology have en-abled more refined evaluations.

In 2006, Buehler estimated the fracturestrength of a TC monomer to be 11 GPa, whichis significantly greater than that of a collagenfibril (0.5 GPa) (102). This difference is rea-sonable, given that fracture of a TC monomerrequires unraveling of the triple helix and ul-timately breaking of covalent bonds, whereasfracture of a fibril does not necessarily requirethe disruption of covalent bonds. For compar-ison, the tensile strength of collagen in tendonis estimated to be 100 MPa (120).

The Young’s modulus of a TC monomer isE = 6–7 GPa (102, 121), whereas AFM mea-surements show that dehydrated fibrils of typeI collagen from bovine Achilles tendon (122)and rat tail tendon (123) have E ≈ 5 GPa andE ≤ 11 GPa, respectively. Because collagen fib-rils are anisotropic, the shear modulus (which isa measure of rigidity) is also an important mea-sure of the strength of a collagen fibril. In 2008,AFM revealed that dehydrated fibrils of typeI collagen from bovine Achilles tendon haveG = 33 MPa (124). Hydration of these fib-rils reduced their shear modulus significantly,whereas carbodiimide-mediated cross-linkingincreased their shear modulus. It is notewor-thy that a certain level of cross-linking is favor-able for the mechanical properties of collagenfibrils, but excessive cross-linking results in ex-tremely brittle collagen fibrils (102), a commonsymptom of aging.

An analysis by Buehler (102) of the me-chanical properties of collagen fibrils sug-gests that nature has selected a length for theTC monomer that maximizes the robustnessof the assembled collagen fibril via efficientenergy dissipation. Simulations indicate thatTC monomers either longer or shorter than∼300 nm (which is the length of a type I col-lagen triple helix) would form collagen fibrilswith less favorable mechanical properties.

COLLAGENOUS BIOMATERIALS

Research on the structure and stability of colla-gen triple helices has focused on blunt-ended

triple helices composed of (XaaYaaGly)n≤10

CRPs. These short triple helices, althoughvaluable for studies directed at understandingthe physicochemical basis of triple-helix struc-ture and stability, are not useful for many po-tential biomaterial applications because of theirsmall size, which does not approach the scale ofnatural collagen fibers (Figure 2).

Bovine collagen is readily available and use-ful for some biomedical purposes, but it suffersfrom heterogeneity, potential immunogenic-ity, and loss of structural integrity during theisolation process. An efficient recombinant orsynthetic source of collagen could avoid thesecomplications. The heterologous productionof collagen is made problematic by the diffi-culty of incorporating posttranslational modi-fications, such as that leading to the essentialHyp residues (Figure 6), and by the needto use complex expression systems (125).These challenges underscore the need for syn-thetic sources of collagen-like proteins andfibrils.

Collagen via Chemical Synthesis

Early approaches to long synthetic collagentriple helices relied on the condensation (126,127) or native chemical ligation of shortCRPs (127). Interestingly, concentrated aque-ous solutions of (ProHypGly)10 self-assembleinto highly branched fibrils (128). Brodskyand coworkers (129) have shown that therate of (ProHypGly)10 self-assembly and themorphology of the resultant fibrils are se-quence dependent. CRPs containing a singlePro→Ala or Pro→Leu substitution displayslower self-assembly; fibril morphology can bemodified by a Gly→Ser substitution, or pre-vented by a single Gly→Ala substitution orglobal Hyp→Pro substitutions. Regardless, thehigher-order structures formed by the self-assembly of (ProHypGly)10 and related CRPsdo not resemble natural collagen fibrils.

Long collagen triple helices have been pre-pared by using a design that takes advantageof the intrinsic propensity of individual CRPstrands to form triple helices. Specifically, a


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cystine knot within short collagen fragmentswas utilized to set the register of individualcollagen strands such that short, “sticky” endspreorganized for further triple-helix formationwere displayed at the end of each triple-helical,monomeric segment (Figure 10a) (130, 131).Self-assembly of these short, triple-helix frag-ments was then mediated by association of thesticky ends, resulting in collagen assemblies aslong as 400 nm—significantly longer than nat-ural TC monomers (131). Koide and cowork-ers (132) used this system to prepare tunablecollagen-like gels with potential biomaterialapplications.

Maryanoff and coworkers (133) developedanother approach to long triple helices, onethat relied on the predilection of electron-richphenyl rings of C-terminal phenylalanineresidues installed in a short CRP to engagein π-stacking interactions preferentially withelectron-poor pentafluorophenyl rings ofN-terminal pentafluorophenylalanine residues(Figure 10b). Their strategy producedmicrometer-scale triple-helical fibers. Thisπ-stacking approach has been used to gen-erate thrombogenic collagen-like fibrils forapplications in biomedicine (134). In addition,attachment of gold nanoparticles to thesefibrils and subsequent electroless silver platingyielded collagen-based nanowires that conductelectricity (135).

Przybyla & Chmielewski (136) used metal-triggered self-assembly to obtain collagen fib-rils from a CRP. A single Hyp residue inAc-(ProHypGly)9-NH2 was replaced with abipyridyl-modified Lys residue. Addition ofFe(II) to a solution of this CRP triggered self-assembly into morphologically diverse fibrils ofup to 5 μm in length with a mean radius of0.5 μm.

A major advance in the development of syn-thetic CRP assemblies with improved similarityto collagen fibrils was reported by Chaikof andcoworkers (137). They synthesized a CRP withthe sequence (ProArgGly)4–(ProHypGly)4–(GluHypGly)4 and observed self-assembly insolution into fibrils 3–4 μm in length and 12–15 nm in diameter. Upon heating the peptide

solution to 75◦C for 40 min and then cooling toroom temperature, they observed thicker fib-rils (∼70 nm in diameter). Importantly, thesefibrils exhibited two key characteristics of natu-ral collagen fibrils. First, the fibrils displayedtapered tips at their termini—a feature ob-served in type I collagen fibers and thought tobe important for fiber growth (138). Second,Chaikof and coworkers observed D-periodicstructure in synthetic collagen fibrils, with D ≈18 nm. The self-assembly process presumablyrelies on Coulombic interactions and hydrogenbonds between charged Arg and Glu residuesin individual, axially staggered triple helices(Figure 10c).

The methodologies described above enablethe creation of long, triple-helical, collagen-like fibrils. Despite major advances, syntheticcollagen-mimetic fibrils still lack many of thecharacteristics of higher-order collagen struc-tures. In addition, the mechanical properties ofsynthetic collagenous materials have not beenstudied to date. Synthetic collagens that closelymimic the length, girth, patterns, mechanicalproperties, and complexity of natural collagenfibrils remain to be developed, but rapidprogress in the past few years engenders greatoptimism.

Biological and BiomedicalApplications of Synthetic Collagen

Relatively few CRPs have been tested as bioma-terials. Goodman and coworkers (139) showedthat peptoid-containing CRPs have a notableability to bind to epithelial cells and fibroblasts,particularly when displayed on a surface. CRPsare also useful for inducing platelet aggrega-tion, which can aid the wound-healing process(140, 141).

A key step toward utilizing collagenous bio-materials for therapeutic purposes is the de-velopment of CRPs that can either adhere toor bury themselves within biological collagen.Most efforts toward these objectives have re-lied on immobilization of CRPs on an unre-lated substance. Yu and coworkers (142) pre-pared CRP-functionalized gold nanoparticles


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b

a

c

H2N

O

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O

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(ProHypGly)5 (ProHypGly)3

(ProHypGly)3

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GlyCysCysGlySelf-assembly

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D ≈ 17.9 nm

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N··· ···CN··· ···C

N··· ···C

OH

Figure 10Strategies for the self-assembly of long, synthetic collagen triple helices and fibrils. (a) Disulfide bondsenforce a strand register with sticky ends that self-assemble (131). (b) Stacking interactions betweenelectron-poor pentafluorophenyl rings and electron-rich phenyl rings lead to self-assembly (133, 134).(c) Coulombic forces between cationic and anionic blocks encourage self-assembly. TEM image of aresulting fiber shows D-periodicity with D = 17.9 nm (137). Natural type I collagen has D = 67 nm.


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and demonstrated binding of the gold nanopar-ticles to the gap region of natural collagen.Maryanoff and coworkers found that CRPsdisplayed on latex nanoparticles can stimu-late human platelet aggregation with a potencysimilar to that of type I collagen (140). In animportant extension of this work, they demon-strated that triple-helical fibrils obtained viaaromatic interactions had a similar level of

thrombogenic activity to the CRPs immobi-lized on latex nanoparticles (134). Finally, sin-gle strands of CRPs and polyethylene glycol-conjugated CRPs bind to collagen films evenwithout immobilization on nanoparticles (143)and are of potential use in collagen imaging(144) and wound-healing applications. The fu-ture of these approaches appears to be especiallybright.

SUMMARY POINTS

1. High-resolution crystal structures and modern biophysical approaches have enabled de-tailed study of the structure and stability of collagen triple helices. The ladder of hydrogenbonds observed in these crystal structures is essential for holding the triple helix together,and its absence in natural collagen leads to a variety of pathological conditions.

2. Stereoelectronic effects impart significant structural stability to collagen by preorganizingindividual polypeptides for triple-helix formation. For example, Hyp in the Yaa positionstabilizes the triple helix via a stereoelectronic effect. Stereoelectronic effects are alsoimportant for the structure and stability of numerous other peptides and proteins.

3. Posttranslational modifications to protocollagen are of fundamental importance to thesynthesis of a stable ECM. These modifications include hydroxylation and cross-linkingreactions.

4. Collagen fibrillogenesis is an essential process for the formation of macromolecularbiological scaffolds. Relatively high-resolution models of type I and type II collagen fib-rils are now available and, for type I collagen, show that collagen fibrils can be describedas nanoscale ropes.

5. Simple means to synthesize long collagen triple helices and fibrils have become apparent.The resultant materials are poised for use in biomedicine and nanotechnology.

FUTURE ISSUES

1. The factors that affect triple-helix stability for Pro derivatives in the Yaa position are nowclear. In comparison, the Xaa position is understood only poorly. What, for example, isthe physicochemical basis for the anomalous effects of hyp and Hyp on triple-helixstability in the Xaa position?

2. The current understanding of triple-helix structure and stability derives from analysesof triple-helical CRPs. Do these analyses provide insight on the stability and mechanicalproperties of natural collagen fibrils?

3. What functionalities in natural collagen are important for proper fibril formation inthe ECM? How might diseases stemming from improper fibril formation be subject totherapeutic intervention?


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4. Can improved methods be developed to synthesize long collagen triple helices and rele-vant mimics of complex, hierarchical collagen assemblies?

5. What are the molecular structures of nonfibrillar collagen assemblies? How are thoseassemblies formed in vivo?

6. Natural collagens appear to engage many other proteins and biomolecules. Which ones?How? Can those interactions be manipulated to treat disease?

7. How can synthetic collagen-based biomaterials lead to expeditious therapies?

DISCLOSURE STATEMENT

The authors are not aware of any affiliations, memberships, funding, or financial holdings thatmight be perceived as affecting the objectivity of this review.

ACKNOWLEDGMENTS

The authors acknowledge Dr. Jeet Kalia for critical reading of the manuscript and Amit Choudharyfor creating Figure 8d. M.D.S. was supported by graduate fellowships from the Departmentof Homeland Security and the Division of Medicinal Chemistry, American Chemical Society.Collagen research in our laboratory is supported by Grant AR044276 (NIH).

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Dalgleish R. 2009. A database of osteogenesis imperfecta and type III collagen mutations.http://www.le.ac.uk/genetics/collagen/

Khoshnoodi J, Cartailler J-P, Alvares K, Veis A, Hudson BG. 2006. Computer-generated an-imation of assembly of type I and type IV collagen for Reference 38. http://www.mc.vanderbilt.edu/cmb/collagen/

Ricard-Blum S, Ruggiero F, van der Rest M. 2005. The collagen superfamily. Top. Curr. Chem.247:35–84

Koide T, Nagata K. 2005. Collagen biosynthesis. Top. Curr. Chem. 247:85–114Greenspan DS. 2005. Biosynthetic processing of collagen molecules. Top. Curr. Chem. 247:149–83Birk DE, Bruckner P. 2005. Collagen suprastructures. Top. Curr. Chem. 247:185–205


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Franzke C-W, Bruckner P, Bruckner-Tuderman L. 2005. Collagenous transmembrane proteins:recent insights into biology and pathology. J. Biol. Chem. 280:4005–8

Myllyharju J. 2003. Prolyl-4-hydroxylases, the key enzymes of collagen biosynthesis. Matrix Biol.22:15–24

Raines RT. 2006. 2005 Emil Thomas Kaiser award. Protein Sci. 15:1219–25

NOTE ADDED IN PROOF

A twenty-ninth form of vertebrate collagen has been found in skin, lung, and intestine. SoderhallC, Marenholz I, Kerscher T, Ruschendorf F, Esparza-Gordillo J, et al. 2007. Variants in a novelepidermal collagen gene (COL29A1) are associated with atopic dermatitis. PLoS Biol. 5:e242


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Annual Review ofBiochemistry

Volume 78, 2009

ContentsPreface � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �v

Prefatory Articles

FrontispieceE. Peter Geiduschek � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �xii

Without a License, or Accidents Waiting to HappenE. Peter Geiduschek � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 1

FrontispieceJames C. Wang � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �30

A Journey in the World of DNA Rings and BeyondJames C. Wang � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �31

Biochemistry and Disease Theme

The Biochemistry of Disease: Desperately Seeking SyzygyJohn W. Kozarich � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �55

Biosynthesis of Phosphonic and Phosphinic Acid Natural ProductsWilliam W. Metcalf and Wilfred A. van der Donk � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �65

New Antivirals and Drug ResistancePeter M. Colman � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �95

Multidrug Resistance in BacteriaHiroshi Nikaido � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 119

Conformational Pathology of the Serpins: Themes, Variations,and Therapeutic StrategiesBibek Gooptu and David A. Lomas � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 147

Getting a Grip on Prions: Oligomers, Amyloids, and PathologicalMembrane InteractionsByron Caughey, Gerald S. Baron, Bruce Chesebro, and Martin Jeffrey � � � � � � � � � � � � � � � � � 177

Ubiquitin-Mediated Protein Regulation

RING Domain E3 Ubiquitin LigasesRaymond J. Deshaies and Claudio A.P. Joazeiro � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 399

Regulation and Cellular Roles of Ubiquitin-SpecificDeubiquitinating EnzymesFrancisca E. Reyes-Turcu, Karen H. Ventii, and Keith D. Wilkinson � � � � � � � � � � � � � � � � � � � � 363

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Recognition and Processing of Ubiquitin-Protein Conjugatesby the ProteasomeDaniel Finley � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 477

Degradation of Activated Protein Kinases by UbiquitinationZhimin Lu and Tony Hunter � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 435

The Role of Ubiquitin in NF-κB Regulatory PathwaysBrian Skaug, Xiaomo Jiang, and Zhijian J. Chen � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 769

Biological and Chemical Approaches to Diseases of ProteostasisDeficiencyEvan T. Powers, Richard I. Morimoto, Andrew Dillin, Jeffery W. Kelly,and William E. Balch � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 959

Gene Expression

RNA Polymerase Active Center: The Molecular Engineof TranscriptionEvgeny Nudler � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 335

Genome-Wide Views of Chromatin StructureOliver J. Rando and Howard Y. Chang � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 245

The Biology of Chromatin Remodeling ComplexesCedric R. Clapier and Bradley R. Cairns � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 273

The Structural and Functional Diversity of Metabolite-BindingRiboswitchesAdam Roth and Ronald R. Breaker � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 305

Lipid and Membrane Biogenesis

Genetic and Biochemical Analysis of Non-Vesicular Lipid TrafficDennis R. Voelker � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 827

Cholesterol 24-Hydroxylase: An Enzyme of Cholesterol Turnoverin the BrainDavid W. Russell, Rebekkah W. Halford, Denise M.O. Ramirez, Rahul Shah,and Tiina Kotti � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �1017

Lipid-Dependent Membrane Protein TopogenesisWilliam Dowhan and Mikhail Bogdanov � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 515

Single-Molecule Studies of the Neuronal SNARE Fusion MachineryAxel T. Brunger, Keith Weninger, Mark Bowen, and Steven Chu � � � � � � � � � � � � � � � � � � � � � � � 903

Mechanisms of EndocytosisGary J. Doherty and Harvey T. McMahon � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 857

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Recent Advances in Biochemistry

Motors, Switches, and Contacts in the ReplisomeSamir M. Hamdan and Charles C. Richardson � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 205

Large-Scale Structural Biology of the Human ProteomeAled Edwards � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 541

Collagen Structure and StabilityMatthew D. Shoulders and Ronald T. Raines � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 929

The Structural and Biochemical Foundations of Thiamin BiosynthesisChristopher T. Jurgenson, Tadhg P. Begley, and Steven E. Ealick � � � � � � � � � � � � � � � � � � � � � � � � 569

Proton-Coupled Electron Transfer in Biology: Results fromSynergistic Studies in Natural and Model SystemsSteven Y. Reece and Daniel G. Nocera � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 673

Mechanism of Mo-Dependent NitrogenaseLance C. Seefeldt, Brian M. Hoffman, and Dennis R. Dean � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 701

Inorganic Polyphosphate: Essential for Growth and SurvivalNarayana N. Rao, Marıa R. Gomez-Garcıa, and Arthur Kornberg � � � � � � � � � � � � � � � � � � � � � 605

Essentials for ATP Synthesis by F1F0 ATP SynthasesChristoph von Ballmoos, Alexander Wiedenmann, and Peter Dimroth � � � � � � � � � � � � � � � � � � 649

The Chemical Biology of Protein PhosphorylationMary Katherine Tarrant and Philip A. Cole � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 797

Sphingosine 1-Phosphate Receptor SignalingHugh Rosen, Pedro J. Gonzalez-Cabrera, M. Germana Sanna, and Steven Brown � � � � 743

The Advent of Near-Atomic Resolution in Single-Particle ElectronMicroscopyYifan Cheng and Thomas Walz � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 723

Super-Resolution Fluorescence MicroscopyBo Huang, Mark Bates, and Xiaowei Zhuang � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � 993

Indexes

Cumulative Index of Contributing Authors, Volumes 74–78 � � � � � � � � � � � � � � � � � � � � � � � � � �1041

Cumulative Index of Chapter Titles, Volumes 74–78 � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � � �1045

Errata

An online log of corrections to Annual Review of Biochemistry articles may be found athttp://biochem.annualreviews.org/errata.shtml

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